Examples with VCMetaData cbit.vcell.biomodel.meta.VCMetaData used on opensource projects

Example 16 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class ObservablePropertiesPanel method updateInterface.

private void updateInterface() {
    boolean bNonNullObservable = observable != null && bioModel != null;
    // annotationTextArea.setEditable(bNonNullObservable);
    if (bNonNullObservable) {
        VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
    // annotationTextArea.setText(vcMetaData.getFreeTextAnnotation(observable));
    } else {
    // annotationTextArea.setText(null);
    }
    updateShape();
}

Example 17 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class DocumentWindow method showEditAnnotationWindow.

// /**
// * Comment
// */
// private void  showBNGWindow() {
// getWindowManager().showBNGWindow();
// }
/**
 * Comment
 */
private void showEditAnnotationWindow() {
    try {
        if (getWindowManager() != null) {
            VCDocument vcDoc = getWindowManager().getVCDocument();
            if (vcDoc != null) {
                try {
                    // initialize fields - different for biomodel and mathmodel, geometry
                    String oldAnnotation = null;
                    if (vcDoc instanceof BioModel) {
                        oldAnnotation = ((BioModel) vcDoc).getVCMetaData().getFreeTextAnnotation((BioModel) vcDoc);
                    } else {
                        oldAnnotation = vcDoc.getDescription();
                    }
                    // show the editor
                    String newAnnotation = DialogUtils.showAnnotationDialog(this, oldAnnotation);
                    if (org.vcell.util.BeanUtils.triggersPropertyChangeEvent(oldAnnotation, newAnnotation)) {
                        // if VCDocument is a Biomodel, set the vcMetadata, else edit VCDoc.description for now
                        if (vcDoc instanceof BioModel) {
                            // update free text annotation in VCMetaData
                            VCMetaData vcMetaData = ((BioModel) vcDoc).getVCMetaData();
                            vcMetaData.setFreeTextAnnotation((BioModel) vcDoc, newAnnotation);
                        } else {
                            // Update VCDocument annotation
                            vcDoc.setDescription(newAnnotation);
                        }
                    }
                } catch (UtilCancelException e) {
                // Do Nothing
                }
            } else {
                throw new Exception("No Document to Edit");
            }
        }
    } catch (Throwable exc) {
        exc.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Failed to edit annotation!\n" + exc.getMessage(), exc);
    }
}

Example 18 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class ReactionRuleKineticsPropertiesPanel method updateInterface.

protected void updateInterface() {
    boolean bNonNullRule = reactionRule != null && bioModel != null;
    // annotationTextArea.setEditable(bNonNullRule);
    // getKineticsTypeComboBox().setEnabled(bNonNullRule);	// TODO: here!!!
    // TODO: here!!!
    getKineticsTypeComboBox().setEnabled(false);
    if (bNonNullRule) {
        // initKineticChoices();
        VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
        // annotationTextArea.setText(vcMetaData.getFreeTextAnnotation(reactionRule));
        nameTextField.setEditable(true);
        nameTextField.setText(reactionRule.getName());
        getKineticsTypeComboBox().setSelectedItem(getRateLawType(reactionRule.getKineticLaw()));
        if (reactionRule.getKineticLaw().getRateLawType() == RateLawType.Saturable) {
            isReversibleCheckBox.setSelected(false);
            isReversibleCheckBox.setEnabled(false);
        } else if (reactionRule.getKineticLaw().getRateLawType() == RateLawType.MichaelisMenten) {
            isReversibleCheckBox.setSelected(false);
            isReversibleCheckBox.setEnabled(false);
        } else {
            // MassAction
            isReversibleCheckBox.setSelected(reactionRule.isReversible());
            isReversibleCheckBox.setEnabled(true);
        }
    } else {
        // annotationTextArea.setText(null);
        nameTextField.setEditable(false);
        nameTextField.setText(null);
        isReversibleCheckBox.setSelected(false);
        isReversibleCheckBox.setEnabled(true);
    }
    listLinkedPathwayObjects();
}

Example 19 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class AnnotationMapping method getRefInfo.

private HashMap<String, String> getRefInfo(BioModel bioModel, Identifiable identifiable) {
    HashMap<String, String> info = new HashMap<String, String>();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
    Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
    if (refGroupMap != null) {
        for (MiriamRefGroup refGroup : refGroupMap.keySet()) {
            MIRIAMQualifier qualifier = refGroupMap.get(refGroup);
            String[] quaTemp = qualifier.toString().split("/");
            String bioQualifier = quaTemp[quaTemp.length - 1];
            bioQualifier = bioQualifier.substring(0, bioQualifier.length() - 1);
            for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
                String refSource = miriamResource.getMiriamURN();
                String[] temp = refSource.split(":");
                String sourceInfo = temp[2] + ":" + bioQualifier;
                String refId = miriamResource.getIdentifier();
                info.put(refId, sourceInfo);
            // System.out.println(refId + "*********" + sourceInfo);
            }
        }
    }
    return info;
}

Example 20 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class PathwayMapping method createMolecularTypeFromBioPaxObject.

// TODO: not in use
// public void createBioModelEntitiesFromBioPaxObjects(BioModel bioModel, Object[] selectedObjects) throws Exception
// {
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity && !(bioPaxObject instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity && !(ctr.getBioPaxObject() instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)ctr.getBioPaxObject());
// }
// }
// }
// 
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity) {
// createSpeciesContextFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// } else if(bioPaxObject instanceof Conversion) {
// createReactionStepsFromBioPaxObject(bioModel, (Conversion)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity) {
// createSpeciesContextFromTableRow(bioModel, (PhysicalEntity)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// } else if(ctr.getBioPaxObject() instanceof Conversion) {
// createReactionStepsFromTableRow(bioModel, (Conversion)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// }
// }
// }
// }
private MolecularType createMolecularTypeFromBioPaxObject(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) {
    String name;
    if (bioPaxObject.getName().size() == 0) {
        name = getSafetyName(bioPaxObject.getID());
    } else {
        name = getSafetyName(bioPaxObject.getName().get(0));
    }
    RbmModelContainer rbmmc = bioModel.getModel().getRbmModelContainer();
    if (rbmmc.getMolecularType(name) != null) {
        // already exists
        MolecularType mt = rbmmc.getMolecularType(name);
        // check whether it links to pathway object, create relationship object if not
        if (!bioModel.getRelationshipModel().isRelationship(mt, bioPaxObject)) {
            RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
            bioModel.getRelationshipModel().addRelationshipObject(ro);
        }
        return mt;
    }
    int numSubunits = 0;
    if (addSubunits) {
        for (String comment : bioPaxObject.getComments()) {
            numSubunits = StringUtils.countMatches(comment, "SUBUNIT:");
        }
    }
    MolecularType mt = new MolecularType(name, bioModel.getModel());
    try {
        for (int i = 0; i < numSubunits; i++) {
            MolecularComponent mc = new MolecularComponent("Subunit" + i);
            mt.addMolecularComponent(mc);
        }
        rbmmc.addMolecularType(mt, true);
        // we know for sure that a relationship can't exist, so we make one
        RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
        bioModel.getRelationshipModel().addRelationshipObject(ro);
    } catch (ModelException | PropertyVetoException e) {
        e.printStackTrace();
    }
    ArrayList<String> commentList = bioPaxObject.getComments();
    final String htmlStart = "<html><font face = \"Arial\"><font size =\"-2\">";
    final String htmlEnd = "</font></font></html>";
    if (commentList != null && !commentList.isEmpty()) {
        String comment = commentList.get(0);
        if (!comment.isEmpty()) {
            String text = FormatDetails(comment);
            mt.setComment(htmlStart + text + htmlEnd);
        }
    } else {
        mt.setComment("");
    }
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    MIRIAMQualifier qualifier = MIRIAMQualifier.MODEL_isDescribedBy;
    ArrayList<Xref> xrefList = bioPaxObject.getxRef();
    for (Xref xref : xrefList) {
        String url = xref.getURL();
        if (url == null || url.isEmpty()) {
            continue;
        }
        System.out.println(xref.getDb() + ": " + xref.getId());
        try {
            HashSet<MiriamResource> miriamResources = new HashSet<MiriamResource>();
            // http://www.ncbi.nlm.nih.gov/protein/NP_005429	unrecognized (not a valid DataType)
            // http://www.uniprot.org/uniprot/P17275			good
            // TODO: find a mechanism to store the unrecognized ones - they often do work
            MiriamResource mr = miriamManager.createMiriamResource(url);
            miriamResources.add(mr);
            miriamManager.addMiriamRefGroup(mt, qualifier, miriamResources);
        } catch (URNParseFailureException e) {
            e.printStackTrace();
        }
        System.out.println(xref.getDisplayName());
    }
    return mt;
}